--- title: "TP53 K164E (c.490A>G, rs879254249) | Dante Labs" description: "ClinVar classifies TP53 K164E as Pathogenic (reviewed by expert panel). Where it sits in the genome, its predicted effect, and the Genome Test reports that look at it." url: "https://dantelabs.com/genes/tp53/variants/k164e" --- 1. [Genes](https://dantelabs.com/genes) 2. [TP53](https://dantelabs.com/genes/tp53) 3. TP53 K164E Variant # TP53 K164E NM_000546.6(TP53):c.490A>G (p.Lys164Glu) Also known as - p.Lys164Glu - p.K164E - rs879254249 * ClinVar classification Pathogenic * Review status 3 stars out of 4 reviewed by expert panel * Last evaluated 5 June 2025 * Expert panel ClinGen TP53 Variant Curation Expert Panel, ClinGen Data current to ClinVar release 2026-10-12 · Dante Labs data release 2026.10.16-c6eea6bf Facts last changed 16 October 2026 ## Summary K164E is a missense variant in TP53: it changes a single amino acid in the protein the gene encodes. ClinVar classifies it as pathogenic for Li-Fraumeni Syndrome (reviewed by expert panel). ## ClinVar classifications | Condition | Classification | Review status | Submissions | Last evaluated | | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------- | ----------------------------------------- | ------------ | -------------- | | [Li-Fraumeni Syndrome](https://dantelabs.com/conditions/li-fraumeni-syndrome) [ClinVar VCV000246416 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/246416/) | Pathogenic | 3 stars out of 4 reviewed by expert panel | 1 submission | 5 June 2025 | Classifications as ClinVar records them in release 2026-10-12. ClinVar updates them as evidence is reviewed. ## Where it lies in TP53 K164E lies in exon 5 of the 11 in TP53's MANE Select transcript, NM_000546.6. [TP53 variants in exon 5 →](https://dantelabs.com/genes/tp53/variants?exon=5) [TP53's gene diagram →](https://dantelabs.com/genes/tp53#gene-structure) ## Molecular details | Gene | [TP53](https://dantelabs.com/genes/tp53) | | --------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------- | | Transcript | NM_000546.6 MANE Select | | Coding DNA change (HGVS c.) | c.490A>G | | Protein change (HGVS p.) | p.Lys164Glu p.K164E | | Predicted consequence | Missense [missense_variant (opens in a new tab)](https://purl.obolibrary.org/obo/SO_0001583) | | Predicted impact | Moderate | | Position (GRCh38) | chr17:7675122 T>C | | Position (GRCh37) | chr17:7578440 T>C | | dbSNP ID | [rs879254249 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/snp/rs879254249) | | ClinVar Variation ID | [VCV000246416 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/246416/) | | ClinVar Allele ID | 245075 | | ClinGen Allele Registry ID | [CA10584591 (opens in a new tab)](https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA10584591) | | ClinVar name | NM_000546.6(TP53):c.490A>G (p.Lys164Glu) | ## TP53 K164E in other databases - [ClinVar VCV000246416 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/246416/) - [dbSNP rs879254249 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/snp/rs879254249) - [ClinGen Allele Registry CA10584591 (opens in a new tab)](https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA10584591) - [gnomAD 17-7675122-T-C (opens in a new tab)](https://gnomad.broadinstitute.org/variant/17-7675122-T-C?dataset=gnomad_r4) - [Ensembl rs879254249 (opens in a new tab)](https://www.ensembl.org/Homo_sapiens/Variation/Explore?v=rs879254249) ## Reports that look at this variant (1) These Genome Test condition reports include K164E among the variants they look at. | Report | Conditions | Inheritance | | ----------------------------------------------------------------------------- | -------------------- | ------------------ | | [Li-Fraumeni Syndrome](https://dantelabs.com/conditions/li-fraumeni-syndrome) | Li-Fraumeni Syndrome | Autosomal dominant | ## Other variants in TP53 - [A138P Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/tp53/variants/a138p) - [A138V Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/tp53/variants/a138v) - [A161_Y163delinsD Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/tp53/variants/a161-y163delinsd) - [A347D Pathogenic 3 stars out of 4](https://dantelabs.com/genes/tp53/variants/a347d) - [c.-29+1G>T Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/tp53/variants/c--29plus1g-t) - [c.97-1G>A Pathogenic 3 stars out of 4](https://dantelabs.com/genes/tp53/variants/c-97-1g-a) - [c.375+5G>A Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/tp53/variants/c-375plus5g-a) - [c.919+1G>A Pathogenic 3 stars out of 4](https://dantelabs.com/genes/tp53/variants/c-919plus1g-a) - [c.993+1del Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/tp53/variants/c-993plus1del) - [C124X Pathogenic 3 stars out of 4](https://dantelabs.com/genes/tp53/variants/c124x) [All TP53 variants](https://dantelabs.com/genes/tp53/variants) ## Limitations This page describes publicly available information about a genetic variant. It is not a diagnosis, and it says nothing about whether you or anyone else carries this variant. Classifications come from ClinVar and change as new evidence is reviewed. A classification here may differ from the one in ClinVar today, or from the one a laboratory reports. Whole genome sequencing with short reads can miss or miscall some variants, particularly in repeated or highly similar stretches of DNA and in large insertions, deletions or rearrangements. If you have questions about a variant in your own results or in your family, talk to a genetic counsellor or your doctor. ## Sources & credits - Classifications from ClinVar (release 2026-10-12), National Center for Biotechnology Information. - Condition terms from the Mondo Disease Ontology (release 2026-10-06), used under CC BY 4.0. - Gene symbols and names from the HUGO Gene Nomenclature Committee (release 2026-10-16). - Allele identifiers from the ClinGen Allele Registry (release 2026-10-16-c4908f54). - Reference SNP identifiers from dbSNP (release b157), National Center for Biotechnology Information. - Gene–disease links from the Gene Curation Coalition, GenCC (release 2026-10-16). - Difficult regions from the Genome in a Bottle Consortium (release v3.6). - Transcripts from MANE (release v1.5), NCBI and EMBL-EBI. - Predicted consequences from mehari (release 0.11.0), with transcript models from cdot. - Built from Dante Labs data release 2026.10.16-c6eea6bf of 16 October 2026. ## Cite this page APA > Dante Labs. (16 October 2026). TP53 K164E (c.490A>G, rs879254249) (Version 2026.10.16-c6eea6bf). Retrieved 16 October 2026, from https\://dantelabs.com/genes/tp53/variants/k164e Vancouver > Dante Labs. TP53 K164E (c.490A>G, rs879254249) \[Internet]. Version 2026.10.16-c6eea6bf. 16 October 2026 \[cited 16 October 2026]. Available from: https\://dantelabs.com/genes/tp53/variants/k164e Download citation [RIS](https://dantelabs.com/genes/tp53/variants/k164e/cite.ris) [BibTeX](https://dantelabs.com/genes/tp53/variants/k164e/cite.bib) [CSL-JSON](https://dantelabs.com/genes/tp53/variants/k164e/cite.json) ## Read your whole genome From $449 Free shipping · Results in 6–8 weeks [Explore the Genome Test](https://dantelabs.com/whole-genome-sequencing)